Given the nature of the spell Comprehend Languages in Pathfinder, is there any particular advantage to taking Linguistics for a character who can cast it? Especially given the chance of severe (or horribly entertaining, depending on your point of view) failure with Linguistics that doesn't seem to exist for Comprehend Languages.

The spell changed in Pathfinder from comprehend languages in Dungeons and Dragons 3.5. In the Pathfinder antecedent the caster "must touch the creature" that is to be comprehended--which is much riskier and, potentially, socially awkward.
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Hey I Can ChanJul 30 '14 at 12:16

@GMJoe answered quite well, so I'll just add an additional comment: Comprehend Languages / Tongues tends gives literal translations, but does not grant you understanding of idioms. Linguistics has the important extra knowledge so you don't say 'fire it up' in gnomish to a gnome and he looks at you like you're crazy because why do you want to set his invention on fire?!
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Wolfman JoeJul 30 '14 at 14:37

5 Answers
5

This has come up in one of the campaign I currently run. Comprehend languages, like most spells, has a limited duration and is therefore only useful as long as:

You don't encounter more than one piece of foreign-language text over the course of the day.

The foreign-languages you do encounter can be completely interpreted before the duration runs out.

Of course, players could prepare the spell more than once, but then they find themselves short on spell slots. Charged magic items can offset the disadvantage of spells without requiring slots, but they tend to have a worryingly large up-front cost for a non-guaranteed payoff.

The problem with translation spells is exacerbated by the fact that memories are rarely perfect: A wizard who read the riddle-poem of Llasynt the Long-winded probably won't remember it word for word, and if guessing the password for Llasynt's front door requires the third verb in the fourth insulting stanza, then he'd better have made some detailed notes...

Linguistics, on the other hand is always on, is non-magical (and therefore works in situations where magic would be impossible, inadvisable or a social faux pas), and makes you a hit at parties. It also doesn't require you to touch the target for it to work, which again may allow you to avoid potential hazards, inconvenient distances, and more social faux pas. Plus, it grants you an additional language known with each rank, which is a nice way to avoid making mistakes with the skill entirely.

GMJoe has a great answer, but there's one major reason that comprehend languages is not a good solution that everyone else has missed.

From the spell:

You can understand the spoken words of creatures or read otherwise incomprehensible written messages. The ability to read does not necessarily impart insight into the material, merely its literal meaning. The spell enables you to understand or read an unknown language, not speak or write it.

Comprehend languages is a one-way spell. It's useless if you need to actually communicate in the alternate language, rather than just understanding what someone says. Tongues does provide that ability, but it's 3rd/4th level spell.

You can decipher writing in an unfamiliar language or a message written in an incomplete or archaic form.

With Linguistics, you get the language, its history and past forms, and contextual knowledge to fill in blanks. You do not get this with Comprehend or Tongues. Such is the reward for spending skill points.

Additionally, Linguistics is used to create and detect forgeries. Either of those uses can be extremely useful.

And since the problem will arise, what about Linguistics vs permanent Tongues, or an equivalent item? Basically, the thing is that one of the often forgotten points of Linguistics is that it is not useful only to speak/understand a language. It also represents how deeply you understand this language, etc. It can be seen as Knowledge: languages from this aspect.

For example, someone with Tongues/Comprehend Languages would be able to speak/understand French, sure. Ask him for the etymology of one word, and he is screwed, he just doesn't have the knowledge at all. On the same note, he probably has no idea how the grammar/conjugations works. It also mean that if he encounter some kind of slang, he won't be able to speak it, as he has a global understanding of the language, not of his workings/adaptations.

Our brave band of fearless heroes have braved the Chasm of Doom, crossed the Bridge of Tears and found their way to the Orc lair, from which they can make out some grunting in the fiendishly difficult greenskin tongue.

"What are they saying?", whispered Mik Half-finger.

His elven companion smiled and spent a few seconds incanting.

"They are saying…"

"Yes?", prompted Mik eagerly.

"They are saying that someone is casting magic behind this wall."

"Then shoot them with a magic missile!"

"I can't! I memorised Comprehend Languages this morning!"

"Ruuuuuuuuun!"

Comprehend Languages requires time (sound, spell components, etc) to cast and uses up a spell slot.